GeneNetworkBuilder: Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data

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Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

Author
Jianhong Ou , Haibo Liu, Heidi A Tissenbaum and Lihua Julie Zhu
Date of publication
None
Maintainer
Jianhong Ou <jianhong.ou@umassmed.edu>
License
GPL (>= 2)
Version
1.16.0

View on Bioconductor

Man pages

buildNetwork
construct the regulatory network
ce.IDsMap
map file for converting gene name or sequence name of...
ce.interactionmap
transcript regulatory map of _Caenorhabditis elegans_
ce.mapIDs
map file for converting from wormbase identifier to...
ce.miRNA.map
micro RNA of _Caenorhabditis elegans_
convertID
convert gene IDs by id map
example.data
example datasets for documentation
filterNetwork
filter the regulatory network table by expression profile
hs.IDsMap
map file for converting gene name or sequence name of _Homo...
hs.interactionmap
transcript regulation map of _Homo sapiens_
hs.mapIDs
map file for converting from Entrez identifier to _Homo...
hs.miRNA.map
micro RNA of _Homo sapiens_
polishNetwork
generate an object of grahpNEL to represent the regulation...
uniqueExprsData
unique the microarray data

Files in this package

GeneNetworkBuilder/.BBSoptions
GeneNetworkBuilder/DESCRIPTION
GeneNetworkBuilder/NAMESPACE
GeneNetworkBuilder/NEWS
GeneNetworkBuilder/R
GeneNetworkBuilder/R/GeneNetworkBuilder.R
GeneNetworkBuilder/R/applications.R
GeneNetworkBuilder/build
GeneNetworkBuilder/build/vignette.rds
GeneNetworkBuilder/data
GeneNetworkBuilder/data/ce.IDsMap.rda
GeneNetworkBuilder/data/ce.interactionmap.rda
GeneNetworkBuilder/data/ce.mapIDs.rda
GeneNetworkBuilder/data/ce.miRNA.map.rda
GeneNetworkBuilder/data/datalist
GeneNetworkBuilder/data/example.data.rda
GeneNetworkBuilder/data/hs.IDsMap.rda
GeneNetworkBuilder/data/hs.interactionmap.rda
GeneNetworkBuilder/data/hs.mapIDs.rda
GeneNetworkBuilder/data/hs.miRNA.map.rda
GeneNetworkBuilder/inst
GeneNetworkBuilder/inst/doc
GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.R
GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.Rnw
GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.pdf
GeneNetworkBuilder/inst/unitTests
GeneNetworkBuilder/inst/unitTests/test_geneNetworkBuilder.R
GeneNetworkBuilder/man
GeneNetworkBuilder/man/buildNetwork.Rd
GeneNetworkBuilder/man/ce.IDsMap.Rd
GeneNetworkBuilder/man/ce.interactionmap.Rd
GeneNetworkBuilder/man/ce.mapIDs.Rd
GeneNetworkBuilder/man/ce.miRNA.map.Rd
GeneNetworkBuilder/man/convertID.Rd
GeneNetworkBuilder/man/example.data.Rd
GeneNetworkBuilder/man/filterNetwork.Rd
GeneNetworkBuilder/man/hs.IDsMap.Rd
GeneNetworkBuilder/man/hs.interactionmap.Rd
GeneNetworkBuilder/man/hs.mapIDs.Rd
GeneNetworkBuilder/man/hs.miRNA.map.Rd
GeneNetworkBuilder/man/polishNetwork.Rd
GeneNetworkBuilder/man/uniqueExprsData.Rd
GeneNetworkBuilder/src
GeneNetworkBuilder/src/Makevars
GeneNetworkBuilder/src/Makevars.win
GeneNetworkBuilder/src/geneTree.cpp
GeneNetworkBuilder/src/geneTree.h
GeneNetworkBuilder/src/nodefilter.cpp
GeneNetworkBuilder/tests
GeneNetworkBuilder/tests/runTests.R
GeneNetworkBuilder/vignettes
GeneNetworkBuilder/vignettes/GeneNetworkBuilder.Rnw
GeneNetworkBuilder/vignettes/hs_sample_rcytoscape.eps
GeneNetworkBuilder/vignettes/hs_sample_rcytoscape.pdf
GeneNetworkBuilder/vignettes/workflow.eps
GeneNetworkBuilder/vignettes/workflow.pdf